I assume a fuel processor can handle water and methane as gas giants have both.
You don't need a fuel processor to obtain hydrogen from gas giant scooping, only scoops. Unrefined fuel has historically been poorly defined, but Mongoose very clearly states to be liquid hydrogen, with trace impurities. If it was
anything else, unrefined fuel and refined fuel would need different fuel tanks and have a different mass to volume ratio.
Refining turns that into liquid hydrogen of much higher purity. The SOM discusses this in some detail and basically says that while fusion plants don't care about refined or unrefined fuel, jump drives are sensitive to it, because the fuel is used to physically inflate the jump bubble and monatomic hydrogen is the best thing to use:
The section doesn't outright state it, but it seems to me that the impurities that cause issues would include deuterium and tritium. Unrefined fuel probably doesn't contain many big molecules, but might have a fair bit of deuterium. It occurs naturally at 0.015% of all hydrogen.
For me, Refined fuel just being liquid hydrogen with the deuterium removed makes a deal of sense.
Mongoose at least have laid down a consistent explanation, including that jump field and jump grid are just alternate ways to create the bubble, but both still need injected mass to inflate it. That does mean abandoning the option for pure battery powered jump, or shunting it to different tech, but I'm okay with that.
